RISM-FF

RISM Force Field program: assign a force field to a molecule and create the rism input file



Download:


*Update*

File with the OPLS patterns.
Currently supported:
- alkanes
- alcohols (COH)
- ethers (COC)
- acetals (OCO)
- carboxilate (COOH) group
- carboxilate ion (COO-)
- benzene (C6H6)
- phenyl C6H5R




How To Install:

• download

• unpack:

tar -xzf rismff_2012_03_09.tar.gz

• go to installation folder

cd rismff_2012_03_09.tar.gz

• make all

./makeAll

• add to PATH

export PATH=$PATH:$(pwd)
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc

* NOTE: you will in any case need to provide the full paths to the sigmas.dat, ffopls.pat and ffoplsaabn.itp files, or copy them to the folder where you are going to use the rism_ff


How to Use

You should have pdb or xyz coordinates of your molecule.

For simplicity, let we have molecule.pdb file

Also, you need
- the atom radii file (sigmas.dat)
- the force-field patterns file (ffopls.pat)
- the gromacs nonbonded itp foce-field file (ffoplsaanb.itp)

All these files are provided with the program.

To assign the force-field to the molecule do the following steps:

1) convert the coordinates to atom pattern (connections) file:

./coors2pat molecule,pdb sigmas.dat > molecule.pat

2) assign the force-field file types usign the force-field patterns:

./assignAtomTypes molecule.pat ffopls.pat > moleculeAT.pat

3) convert the molecule to the RISM format

./createRismInput molecule.pdb moleculeAT.pat ffoplsaanb.itp > molecule.rism

For details - please read the help messages for the programs ./coors2pat, ./assignAtomTypes, ./createRismInput (just run them without arguments to see the help)
Also, please read the comments in the begining of ffopls.pat file.


Example:
with the program is distributed the file neopentane.pdb
Go to the instalation folder, and do the following:

./coors2pat neopentane.pdb | tee neopentane.pat
./assignAtomTypes neopentane.pat | tee neopentaneAT.pat
./createRismInput neopentane.pdb neopentaneAT.pat | tee neopentane.rism